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StochasticAnalytics / emClarity

GNU Lesser General Public License v3.0
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Help needed in China, no access to google drive... #72

Closed hgxy15 closed 5 years ago

hgxy15 commented 5 years ago

Hi, Ben, I just heard the talk on emClarity on Kuo Symposium, Fantastic results! really eager to try this software on my data set, but I currently have no access to google drive in china, is there any other way emClarity is distributed? Many thanks in advance!

Gaoxing

bHimes commented 5 years ago

Hi Gaoxing,

Do you have a Matlab license? I could write a brief guide on compiling from the source code.

Otherwise, we can figure something else out.

Ben

On Wed, Sep 5, 2018, 2:53 AM hgxy15 notifications@github.com wrote:

Hi, Ben, I just heard the talk on emClarity on Kuo Symposium, Fantastic results! really eager to try this software on my data set, but I currently have no access to google drive in china, is there any other way emClarity is distributed? Many thanks in advance!

Gaoxing

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hgxy15 commented 5 years ago

I do have a matlab license, I tried using the mCompile.sh emClarity.m to install the emClarity from source code, but when I type ./emClarity_gaoxing_1_0_0 in the bin directory, the program gives the following error: Index exceeds array bounds.

Error in emClarity (line 8)

MATLAB:badsubscript Is there something I'm missing here?

Gaoxing

hgxy15 commented 5 years ago

I'm currently using Matlab 2018a and the MCR I installed is also the 2018Ra version. The cuda version is cuda9.1.

bHimes commented 5 years ago

Hi Gaoxing,

So I haven't tested yet on 2018 versions of matlab, and while it should work based on what I remember reading on the release notes, I can only say that it will work for release 2017b

Did you compile on your own using mcc or did you run the following in your testScripts dir? I assume you did.

.../testScripts ] $ > ./mCompile emClarity

After emClarity is compiled, you can't call the binary directly, rather you must use the shell script provided, which in this case is called emClarity_17b. This script is also generated by the mCompile shell script when you use it to compile the code.

Alternatively, you could try running emClarity from within an interactive session in matlab. I provided some instructions on this sometime in the last week, and you should be able to search for that message in the emClarity google group archive.

Let me know if either of those solutions work, or if you need more specific instructions on how to carry them out.

Best,

ben

Benjamin Himes

cryoEM methods development Grigorieff lab https://mail.hhmi.org/owa/redir.aspx?C=SbsCefkcbOt75jDyr05lpd3OifVN_utmfvnhZrtXS7Bl2i2eOXXVCA..&URL=http%3a%2f%2fgrigoriefflab.janelia.org%2f, HHMI Janelia Research Campus

cryoSTAC development @ emClarity https://mail.hhmi.org/owa/redir.aspx?C=8yDzXj54yTidMevTB7q5m3liEVwqAZ9LxuXQ4iYOVvtl2i2eOXXVCA..&URL=https%3a%2f%2fgithub.com%2fbHimes%2femClarity%2fwiki

On Wed, Sep 5, 2018 at 8:52 AM hgxy15 notifications@github.com wrote:

I'm currently using Matlab 2018a and the MCR I installed is also the 2018Ra version. The cuda version is cuda9.1.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bHimes/emClarity/issues/72#issuecomment-418719036, or mute the thread https://github.com/notifications/unsubscribe-auth/AC71mEo47GdjUX09MfIDRd6UXXm7Eli4ks5uX8j9gaJpZM4WaSWZ .

hgxy15 commented 5 years ago

Hi, Ben, many thanks for the instruction! Yes, I did run ./mCompile emClarity in the Testscripts directory and I find the emClarity_17b (in this case called emClarity_gaoxing_17b) in the bin directory. However, when I run emClarity_gaoxing_17b, the program gives the following error:

    ***************************************

emClarity version fa82c80 run starting on 06-Sep-2018 09:54:53 cmd 

    ***************************************

Error using emClarity (line 40) \n\n\tRun with help for a list of functions\n\n

Best, Gaoxing

bHimes commented 5 years ago

Hi Gaoxing,

emClarity is really just a command line wrapper to my 3d gpu-accelerated image processing library. It seems maybe you are hoping for a GUI to pop up when you run "emClarity" ?

I would place a softlink in your local bin directory so that running

$ emClarity

actually calls your "emClarity_gaoxing_17b"

Then you could run

$ emClarity check

verify your installation

$ emClarity help

for a list of functions

$ emClarity

to carry out various operations as described in the documentation

(emClarity/docs)

HTH

Ben

On Wed, Sep 5, 2018, 10:02 PM hgxy15 notifications@github.com wrote:

Hi, Ben, many thanks for the instruction! Yes, I did run ./mCompile emClarity in the Testscripts directory and I find the emClarity_17b (in this case called emClarity_gaoxing_17b) in the bin directory. However, when I run emClarity_gaoxing_17b, the program gives the following error:

emClarity version fa82c80 https://github.com/bHimes/emClarity/commit/fa82c80ee4e2d0084468337c9143fc00d662dd9c run starting on 06-Sep-2018 09:54:53 cmd

Error using emClarity (line 40) \n\n\tRun with help for a list of functions\n\n

Best, Gaoxing

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hgxy15 commented 5 years ago

Hi, Ben, Thanks for the help ! I just managed to find a way to gain access to the google drive and obtained the binary distribution, I think the binary is looking for MCR9.3 which is for R2017b,so I'm know installing Matlab 2017b on a different machine, I don't know if there's any way to change this or is this specified during compilation ? Best, Gaoxing

bHimes commented 5 years ago

Hi Gaoxing,

The Matlab compile runtime (MCR) version is entirely dependent on the version of Matlab used at compile time.

The only way to change the MCR required, is to compile it yourself from source using a different Matlab version.

Ben

On Thu, Sep 6, 2018, 8:05 AM hgxy15 notifications@github.com wrote:

Hi, Ben, Thanks for the help ! I just managed to find a way to gain access to the google drive and obtained the binary distribution, I think the binary is looking for MCR9.3 which is for R2017b,so I'm know installing Matlab 2017b on a different machine, I don't know if there's any way to change this or is this specified during compilation ? Best, Gaoxing

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hgxy15 commented 5 years ago

Hi Ben,

Many thanks for the help! I now have emClarity running on a R2017b version of MATLAB with MCR 9.3. I 'm still going through the tutorial, will keep you updated if anything good comes up.

Best, Gaoxing